From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Dec 02 2009 - 15:17:05 CST

Hi,

The topology for water is included in rbcg-2007.top, so you can simply
use that.

Best,
Bin

On Dec 2, 2009, at 12:42 PM, Francesco Pietra wrote:

> Hello Bin:
> I lack an appropriate "water.top", not included in the files that
> Anton posted. The only file with such a name here is for
> MARTINI-GROMACS. Could you please send it?
> thanks
> francesco
>
> On Wed, Dec 2, 2009 at 9:03 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>> Dear francesco:
>>
>> I think the procedure to build a rbcg model should be basically the
>> same as
>> an atomistic one.
>> 1 : obtain the coordinates for your membrane, or protein. This can
>> be done
>> by coarse graining all-atom model using cgtools plugin.
>> 2 : solvate the system using cgsolvate.tcl
>> 3 : add ions to the system.
>> About your "cgsolvate.tcl" problem, I think the reason u get the
>> error:
>> conflicting versions provided for package "solvate": 1.3, then 1.2.
>> is not because the conflict with VMD 1.8.7, but you already type
>> "package
>> require solvate" before the command "source ${script_dir}/
>> cgsolvate.tcl".
>> Try to open a new fresh VMD console, and type "source
>> ${script_dir}/cgsolvate.tcl".
>> But you do need to change the following lines in the cgsolvate.tcl
>> file to
>> provide correct directory:
>> 154 readpsf /Projects/anton/ReducedModels/CG/dat/CGSOLV/cgwat.psf
>> 155 coordpdb /Projects/anton/ReducedModels/CG/dat/CGSOLV/
>> cgwat.pdb
>> 194 topology /home/amyshih/CGSOLV/water.top
>> Hope this helps,
>> Bin
>> On Dec 2, 2009, at 10:13 AM, Francesco Pietra wrote:
>>
>> Hi;
>> After I posted the subject problem as secondary matter, I carried out
>> an accurate search on the web, unable to find an equilibrated rbcg
>> lipid bilayer for vmd 1.8.7/namd martini implementation (or a plain
>> procedure to get it from scratch). As for sbcg, I guess that direct
>> conversion from an equilibrated all-atoms lipid bilayer will not
>> work.
>> Thanks for info.
>> francesco pietra
>>
>>